Emerging role of different DNA methyltransferases in the pathogenesis of cancer

Plasma DNMT1 Activity for Assessing Tumor Burden and Predicting Neoadjuvant Therapy Response in Breast Cancer

DNA methylation is mediated by DNA methyltransferases (DNMTs), and the stability of their activity is essential for cellular fate. DNMT1 is considered one of the most promising targets for research. However, current detection techniques are limited in accurately quantifying its activity in peripheral blood. Here, a reaction system is developed known as DNMT1 Identification by Variable Activity (DIVA) for the highly sensitive detection of DNMT1 activity in the peripheral blood of breast cancer patients. DIVA can detect DNMT1 at levels as low as 10-7 U mL-1, with minimal time and cost. This method is applied to analyze 271 clinical samples, successfully evaluating tumor burden in patients staged I-IV. Finally, this method is utilized to assess the prognosis of 22 patients undergoing neoadjuvant therapy, demonstrating good consistency with ultrasound imaging results. It is believed that DIVA could serve as an effective auxiliary technique for both the early detection of breast cancer and evaluation of neoadjuvant therapy.

The association between DNA methylation status and Epstein-Barr virus infection in laryngeal carcinomas

INTRODUCTION

Infection with Epstein-Barr virus is a known risk factor for laryngeal carcinogenesis; it might influence DNA methylation acting as an epigenetic driver in this type of malignancy.

METHODS

Paired laryngeal tissues (neoplastic and peri-neoplastic) harvested from 24 patients were included in the study. Eleven patients expressing latent/lytic EBV genes were considered positive. 5-mC% was determined using ELISA technique and TSGs (PDLIM4, WIF1, DAPK1) promoters' methylation percentages were quantified by qMS-PCR. DNMTs (DNMT1 and DNMT3B) expression levels were quantified in qRT-PCR.

RESULTS

Overall, in laryngeal neoplastic samples vs peri-neoplastic ones, lower 5mC% (p=0.004) and higher TSGs promoters hypermethylation were found (p<0.0001). Significant correlation between PDLIM4 and DAPK1 promoter methylation and 5-mC% (PDLIM4 p=0.0186; DAPK1 p=0.0259) was noted. Higher 5-mC% (p=0.0041), lower PDLIM4 gene promoter methylation (p=0.0017) and overexpression of DNMTs (DNMT1: p=0.0018, respectively DNMT3B: p=0.0017) were associated with EBV infection. Also, significant differences between EBV-positive and EBV-negative cases based on tumor stage (T) were noted for 5mC% in both T1/T2 (p=0.0364) and T3/T4 stages (p=0.0275), and for PDLIM4 promoter methylation in T1/T2 stages (p=0.0121).

CONCLUSION

Future studies are needed to more effectively illustrate the interplay between EBV infection and these epigenetic mechanisms. Notably, our study highlighted a correlation between EBV and epigenetic changes in laryngeal carcinoma.

Epigenetic and biogenetic regulation by polyphenols in prostate cancer in the context of 3P medicine

Prostate cancer (PCa) can remain asymptomatic for years, complicating early detection and effective intervention. Predictive, Preventive, and Personalized Medicine (3PM) provides a transformative framework for addressing these challenges by integrating novel biomarkers, targeted prevention, and individualized therapies. Recent studies highlight the pivotal role of dysregulated microRNAs (miRNAs) and epigenetic alterations in cancer progression and metastasis. miRNAs, as non-coding RNAs approximately 22 nucleotides in length, regulate gene expression through translational inhibition or mRNA degradation. Dysregulated miRNAs are linked to the overexpression of oncogenic proteins and suppression of tumor suppressor genes in malignancies. Polyphenols such as curcumin, quercetin, resveratrol, and green tea catechins (EGCG) have demonstrated potential in modulating miRNA expression and reversing aberrant epigenetic modifications. Despite their established anticancer effects, the clinical application of polyphenols in stratified patient groups, particularly in primary and secondary cancer prevention, remains underexplored. Beyond their anti-inflammatory and antioxidant properties, polyphenols modulate early epigenetic and biogenetic events critical for cancer prevention and therapy. By targeting predictive biomarkers and improving therapy response, polyphenols contribute significantly to 3PM by enabling early diagnostics, mitigating risks, and personalizing treatments. This review evaluates current knowledge of polyphenols' impact on miRNAs and epigenetics in PCa and explores their potential applications within the 3PM framework, emphasizing predictive diagnostics, targeted prevention, and personalized treatment strategies.

DNA methylation and immune evasion in triple-negative breast cancer: challenges and therapeutic opportunities

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer characterized by the lack of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). Chemotherapy remains the primary treatment option, yet TNBC frequently develops resistance, leading to relapse and metastasis. Emerging evidence highlights the potential of combining DNA methylation inhibitors with immune checkpoint inhibitors (ICIs). DNA methylation contributes to immune escape by silencing immune-regulatory genes, thereby reducing the tumor's visibility to immune cells. Reversing this epigenetic modification can reinvigorate immune surveillance and enhance the efficacy of immunotherapies. This review discusses the role of DNA methylation in TNBC progression and immune evasion, focusing on recent advances in combination therapies involving DNA methylation inhibitors and ICIs. We discuss the underlying mechanisms that enable these therapeutic synergies, preclinical and clinical evidence supporting the approach, and the challenges posed by tumor heterogeneity, drug resistance, and toxicity. Finally, we explore the potential for personalized treatment strategies incorporating multi-omics data to optimize therapeutic outcomes. The integration of epigenetic therapies and immunotherapy offers a promising avenue for improving survival in TNBC patients.

The role of lncRNAs in the interplay of signaling pathways and epigenetic mechanisms in glioma

Gliomas, highly aggressive tumors of the central nervous system, present overwhelming challenges due to their heterogeneity and therapeutic resistance. Glioblastoma multiforme (GBM), the most malignant form, underscores this clinical urgency due to dismal prognosis despite aggressive treatment regimens. Recent advances in cancer research revealed signaling pathways and epigenetic mechanisms that intricately govern glioma progression, offering multifaceted targets for therapeutic intervention. This review explores the dynamic interplay between signaling events and epigenetic regulation in the context of glioma, with a particular focus on the crucial roles played by non-coding RNAs (ncRNAs). Through direct and indirect epigenetic targeting, ncRNAs emerge as key regulators shaping the molecular landscape of glioblastoma across its various stages. By dissecting these intricate regulatory networks, novel and patient-tailored therapeutic strategies could be devised to improve patient outcomes with this devastating disease.

DNMT3a promotes LUAD cell proliferation and metastasis by activating the HDAC7 signalling pathway

Background: Changes in DNA methylation patterns, in which DNA methyltransferases such as DNA methyltransferase 3 alpha (DNMT3a) play important roles, are closely related to the occurrence and development of tumours. However, the role and mechanism of DNMT3a in lung adenocarcinoma (LUAD) remain unknown. The aim of this study was to investigate the potential effect of DNMT3a on LUAD cell proliferation and metastasis and explore the underlying molecular mechanism. Methods: Immunohistochemistry and Kaplan‒Meier survival analysis were used to investigate the relationship between the expression of DNMT3a and histone deacetylase 7 (HDAC7) and the survival, prognosis and clinicopathological features of patients. The effects of DNMT3a on the proliferation and metastasis of LUAD cells were studied in vivo and in vitro. Recombinant lentivirus-mediated in vitro gene overexpression or knockdown, western blotting, Quantitative real-time polymerase chain reaction (qRT‒PCR) and other methods were used in this study to elucidate the potential molecular mechanisms by which DNMT3a promotes LUAD cell proliferation and metastasis. Results: High expression of DNMT3a or HDAC7 was positively correlated with poor prognosis, high AJCC 8th edition stage, and poor tumour differentiation in LUAD patients. LUAD patients with DNMT3a/HDAC7 co-low expression exhibited the worst prognosis. Upregulation of DNMT3a can promote LUAD cell proliferation and metastasis by upregulating HDAC7 and further activating the expression of downstream mediators ZEB1 and c-Myc. Conversely, overexpression of HDAC7 reversed the attenuation of tumour growth and metastasis and the suppression of c-Myc and ZEB1 expression mediated by downregulation of DNMT3a, further indicating the existence of positive feedback regulation between DNMT3a and HDAC7 in LUAD. Conclusion: Our findings first confirmed that DNMT3a acts as a tumour promoter inducing malignant progression of LUAD by upregulating HDAC7 and further inducing upregulation of ZEB1 and c-Myc. Targeting DNMT3a along with HDAC7 might be a promising therapeutic strategy for LUAD.

Identification of the EBF1/ETS2/KLF2-miR-126-Gene Feed-Forward Loop in Breast Carcinogenesis and Stemness

MicroRNA (miR)-126 is frequently downregulated in malignancies, including breast cancer (BC). Despite its tumor-suppressive role, the mechanisms underlying miR-126 deregulation in BC remain elusive. Through silencing experiments, we identified Early B Cell Factor 1 (EBF1), ETS Proto-Oncogene 2 (ETS2), and Krüppel-Like Factor 2 (KLF2) as pivotal regulators of miR-126 expression. These transcription factors were found to be downregulated in BC due to epigenetic silencing or a "poised but not transcribed" promoter state, impairing miR-126 expression. Gene Ontology analysis of differentially expressed miR-126 target genes in the Cancer Genome Atlas: Breast Invasive Carcinoma (TCGA-BRCA) cohort revealed their involvement in cancer-related pathways, primarily signal transduction, chromatin remodeling/transcription, and differentiation/development. Furthermore, we defined interconnections among transcription factors, miR-126, and target genes, identifying a potential feed-forward loop (FFL) crucial in maintaining cellular identity and preventing the acquisition of stemness properties associated with cancer progression. Our findings propose that the dysregulation of the EBF1/ETS2/KLF2/miR-126 axis disrupts this FFL, promoting oncogenic transformation and progression in BC. This study provides new insights into the molecular mechanisms of miR-126 downregulation in BC and highlights potential targets for therapeutic intervention. Further research is warranted to clarify the role of this FFL in BC, and to identify novel therapeutic strategies aimed at modulating this network as a whole, rather than targeting individual signals, for cancer management.

IMI-driver: Integrating multi-level gene networks and multi-omics for cancer driver gene identification

The identification of cancer driver genes is crucial for early detection, effective therapy, and precision medicine of cancer. Cancer is caused by the dysregulation of several genes at various levels of regulation. However, current techniques only capture a limited amount of regulatory information, which may hinder their efficacy. In this study, we present IMI-driver, a model that integrates multi-omics data into eight biological networks and applies Multi-view Collaborative Network Embedding to embed the gene regulation information from the biological networks into a low-dimensional vector space to identify cancer drivers. We apply IMI-driver to 29 cancer types from The Cancer Genome Atlas (TCGA) and compare its performance with nine other methods on nine benchmark datasets. IMI-driver outperforms the other methods, demonstrating that multi-level network integration enhances prediction accuracy. We also perform a pan-cancer analysis using the genes identified by IMI-driver, which confirms almost all our selected candidate genes as known or potential drivers. Case studies of the new positive genes suggest their roles in cancer development and progression.

Integrated analysis of the role of PR/SET domain 14 in gastric cancer

BACKGROUND

Gastric cancer is one of the most common tumors worldwide, and most patients are deprived of treatment options when diagnosed at advanced stages. PRDM14 has carcinogenic potential in breast and non-small cell lung cancer. however, its role in gastric cancer has not been elucidated.

METHODS

We aimed to elucidate the expression of PRDM14 using pan-cancer analysis. We monitored the expression of PRDM14 in cells and patients using quantitative polymerase chain reaction, western blotting, and immunohistochemistry. We observed that cell phenotypes and regulatory genes were influenced by PRDM14 by silencing PRDM14. We evaluated and validated the value of the PRDM14-derived prognostic model. Finally, we predicted the relationship between PRDM14 and small-molecule drug responses using the Connectivity Map and The Genomics of Drug Sensitivity in Cancer databases.

RESULTS

PRDM14 was significantly overexpressed in gastric cancer, which identified in cell lines and patients' tissues. Silencing the expression of PRDM14 resulted in apoptosis promotion, cell cycle arrest, and inhibition of the growth and migration of GC cells. Functional analysis revealed that PRDM14 acts in epigenetic regulation and modulates multiple DNA methyltransferases or transcription factors. The PRDM14-derived differentially expressed gene prognostic model was validated to reliably predict the patient prognosis. Nomograms (age, sex, and PRDM14-risk score) were used to quantify the probability of survival. PRDM14 was positively correlated with sensitivity to small-molecule drugs such as TPCA-1, PF-56,227, mirin, and linsitinib.

CONCLUSIONS

Collectively, our findings suggest that PRDM14 is a positive regulator of gastric cancer progression. Therefore, it may be a potential therapeutic target for gastric cancer.

DNMT3A Cooperates with YAP/TAZ to Drive Gallbladder Cancer Metastasis

Gallbladder cancer (GBC) is an extremely lethal malignancy with aggressive behaviors, including liver or distant metastasis; however, the underlying mechanisms driving the metastasis of GBC remain poorly understood. In this study, it is found that DNA methyltransferase DNMT3A is highly expressed in GBC tumor tissues compared to matched adjacent normal tissues. Clinicopathological analysis shows that DNMT3A is positively correlated with liver metastasis and poor overall survival outcomes in patients with GBC. Functional analysis confirms that DNMT3A promotes the metastasis of GBC cells in a manner dependent on its DNA methyltransferase activity. Mechanistically, DNMT3A interacts with and is recruited by YAP/TAZ to recognize and access the CpG island within the CDH1 promoter and generates hypermethylation of the CDH1 promoter, which leads to transcriptional silencing of CDH1 and accelerated epithelial-to-mesenchymal transition. Using tissue microarrays, the association between the expression of DNMT3A, YAP/TAZ, and CDH1 is confirmed, which affects the metastatic ability of GBC. These results reveal a novel mechanism through which DNMT3A recruitment by YAP/TAZ guides DNA methylation to drive GBC metastasis and provide insights into the treatment of GBC metastasis by targeting the functional connection between DNMT3A and YAP/TAZ.

DNA mismatch repair system regulates the expression of PD-L1 through DNMTs in cervical cancer

BACKGROUND

Cervical cancer (CC) is a potential clinical application of PD-1/PD-L1 inhibitor. We aimed to study the mechanism of DNA mismatch repair (MMR) system regulating the expression of PD-L1 in CC through DNA methyltransferase (DNMTs).

METHODS

We collected pathological specimens from 118 cases of CC to analyze the relationship between PD-L1 expression and DNMTs in different MMR states. RNA interference (RNAi) technique was used to simulate the formation of CC cell line with MMR deficiency (dMMR) state, and subcutaneous tumor formation experiment was carried out in nude mice to verify the relationship between PD-L1 expression and DNMTs in MMR state.

RESULTS

The PD-L1 positive rate in 118 cases of CC was 58.47%, while the microsatellite instability (MSI) status accounted for 5.93%. There was a significant difference in the expression of PD-L1 between patients within the dMMR and MMR proficient (pMMR) groups (χ2 = 21.405, P < 0.001). Subcutaneous inoculation after infection of Siha cells led to successful tumorigenesis in nude mice, accompanied by a significant increase in the level of PD-L1 expression in the mouse tumors, while the expression level of MLH1 and MSH2 protein decreased significantly. We also found that PD-L1 expression was closely related to the expression of DNMTs.

CONCLUSION

PD-L1 is universal expressed on the surface of CC cells, dMMR status enhances the expression of PD-L1 on the surface of CC cells, dMMR states of CC are related to the demethylation status of the PD-L1 gene promoter region.

The Role of Epigenetic Modifier Mutations in Peripheral T-Cell Lymphomas

Peripheral T-cell lymphomas (PTCLs) are a group of diseases with a low incidence, high degree of heterogeneity, and a dismal prognosis in most cases. Because of the low incidence of these diseases, there have been few therapeutic novelties developed over time. Nevertheless, this fact is changing presently as epigenetic modifiers have been shown to be recurrently mutated in some types of PTCLs, especially in the cases of PTCLs not otherwise specified (PTCL-NOS), T follicular helper (TFH), and angioimmunoblastic T-cell lymphoma (AITL). These have brought about more insight into PTCL biology, especially in the case of PTCLs arising from TFH lymphocytes. From a biological perspective, it has been observed that ten-eleven translocators (TET2) mutated T lymphocytes tend to polarize to TFH, while Tregs lose their inhibitory properties. IDH2 R172 was shown to have inhibitory effects on TET2, mimicking the effects of TET2 mutations, as well as having effects on histone methylation. DNA methyltransferase 3A (DNMT3A) loss-of-function, although it was shown to have opposite effects to TET2 from an inflammatory perspective, was also shown to increase the number of T lymphocyte progenitors. Aside from bringing about more knowledge of PTCL biology, these mutations were shown to increase the sensitivity of PTCLs to certain epigenetic therapies, like hypomethylating agents (HMAs) and histone deacetylase inhibitors (HDACis). Thus, to answer the question from the title of this review: We found the Achilles heel, but only for one of the Achilles.

Comprehensive Analysis of DNA Methyltransferases Expression in Primary and Relapsed Ovarian Carcinoma

BACKGROUND

Despite recent advances in epithelial ovarian carcinoma (EOC) treatment, its recurrence and mortality rates have not improved significantly. DNA hypermethylation has generally been associated with an ominous prognosis and chemotherapy resistance, but the role of DNA methyltransferases (DNMTs) in EOC remains to be investigated.

METHODS

In the current study, we systematically retrieved gene expression data from patients with EOC and studied the immunohistochemical expression of DNMTs in 108 primary and 26 relapsed tumors.

RESULTS

Our results showed that the DNMT1, DNMT3A, DNMT3B and DNMT3L RNA levels were higher and the DNMT2 level was lower in tumors compared to non-neoplastic tissue, and DNMT3A and DNMT2 expression decreased from Stage-II to Stage-IV carcinomas. The proteomic data also suggested that the DNMT1 and DNMT3A levels were increased in the tumors. Similarly, the DNMT1, DNMT3A and DNMT3L protein levels were overexpressed and DNMT2 expression was reduced in high-grade carcinomas compared to non-neoplastic tissue and low-grade tumors. Moreover, DNMT1 and DNMT3L were increased in relapsed tumors compared to their primaries. The DNMT3A, DNMT1 and DNMT3B mRNA levels were correlated with overall survival.

CONCLUSIONS

Our study demonstrates that DNMT1 and DNMT3L are upregulated in primary high-grade EOC and further increase in relapses, whereas DNMT3A is upregulated only in the earlier stages of cancer progression. DNMT2 downregulation highlights the presumed tumor-suppressor activity of this gene in ovarian carcinoma.

The evaluation of chitosan hydrogel based curcumin effect on DNMT1, DNMT3A, DNMT3B, MEG3, HOTAIR gene expression in glioblastoma cell line

BACKGROUND

Cancer is one of the most important causes of death worldwide. Some types of cancer, including glioblastoma, with a high potential for growth, invasion, and resistance to general treatments, chemotherapy, and radiotherapy, have a high potential for recurrence. Many chemical drugs have been used to treat it, but herbal drugs are more effective with fewer side effects; Therefore, this research aims to investigate the effect of curcumin-chitosan nano-complex on the expression of MEG3, HOTAIR, DNMT1, DNMT3A, DNMT3B genes in the glioblastoma cell line.

METHODS

In this research, glioblastoma cell line, PCR and spectrophotometry techniques, MTT test and transmission, field emission transmission, and fluorescent electron microscopes were used.

RESULTS

The morphological examination of the curcumin-chitosan nano-complex was without clumping, and the fluorescent microscope examination showed the nano-complex enters the cell and affects the genes expression. In its bioavailability studies, it was found that it significantly increases the death of cancer cells in a dose- and time-dependent manner. Gene expression tests showed that this nano-complex increased MEG3 gene expression compared to the control group, which is statistically significant (p < 0.05). It also decreased HOTAIR gene expression compared to the control group, which was not statistically significant (p > 0.05). It decreased the expression of DNMT1, DNMT3A, and DNMT3B genes compared to the control group, which is statistically significant (p < 0.05).

CONCLUSION

By using active plant substances such as curcumin, the active demethylation of brain cells can be directed to the path of inhibiting the growth of brain cancer cells and eliminating them.

The Emerging Role of Epigenetics in Metabolism and Endocrinology

Each cell in a multicellular organism has its own phenotype despite sharing the same genome. Epigenetics is a somatic, heritable pattern of gene expression or cellular phenotype mediated by structural changes in chromatin that occur without altering the DNA sequence. Epigenetic modification is an important factor in determining the level and timing of gene expression in response to endogenous and exogenous stimuli. There is also growing evidence concerning the interaction between epigenetics and metabolism. Accordingly, several enzymes that consume vital metabolites as substrates or cofactors are used during the catalysis of epigenetic modification. Therefore, altered metabolism might lead to diseases and pathogenesis, including endocrine disorders and cancer. In addition, it has been demonstrated that epigenetic modification influences the endocrine system and immune response-related pathways. In this regard, epigenetic modification may impact the levels of hormones that are important in regulating growth, development, reproduction, energy balance, and metabolism. Altering the function of the endocrine system has negative health consequences. Furthermore, endocrine disruptors (EDC) have a significant impact on the endocrine system, causing the abnormal functioning of hormones and their receptors, resulting in various diseases and disorders. Overall, this review focuses on the impact of epigenetics on the endocrine system and its interaction with metabolism.